Hi Douglas, I checked the status of each subject once recon-all was completed (by looking in the terminal window before I closed it). Each of my roughly 90 subects had the message "*recon-all -s* subjectID *finished without error*at date and time".
When I look at the recon-all.log file the same message is there at the end. Is there somewhere else where i should look for an error message?? Thank you, Laura On Tue, Dec 17, 2013 at 10:44 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > > For the subject that you were not able to load the annot, did you check > the recon-all log file? Did recon-all complete properly? > doug > > > On 12/17/2013 01:35 PM, Laura Taylor wrote: > >> Hi again, Douglas and freesurfer experts. >> >> Unfortunately my problem cannot be explained by having made manual edits >> and then not finishing recon-all. When I load subjects that I did not >> manually edit, I am either unable to load an annotation file (specifically >> r/lh.aparc.a2009s.annot) at all, or I can load it but have problems with >> the output. When I am able to load an image I get a the same tye-died >> appearing surface for one hemisphere (and it is projected onto the opposite >> hemisphere that the label is for) or I get a proper surface when I load the >> label for the other hemisphere (and it appears on the correct hemisphere). >> >> Can you help at all with this? >> >> Thank you, >> >> Laura >> >> >> On Tue, Dec 10, 2013 at 11:45 AM, Laura Taylor >> <taylor.cnos....@gmail.com<mailto: >> taylor.cnos....@gmail.com>> wrote: >> >> Hi, yes thank you both. That is exactly what the problem was. >> >> Laura >> >> >> On Tue, Dec 10, 2013 at 11:12 AM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> Yep, looks like your annot is out of sync with the surfaces >> >> On 12/10/2013 01:51 PM, Chris Watson wrote: >> > I've seen this happen after making manual edits and then not >> finishing >> > a re-run of recon-all. >> > Chris >> > >> > On 12/10/2013 02:00 PM, Laura Taylor wrote: >> >> Hi, >> >> >> >> I'm trying to load lh.aparc.a2009s.annot onto the lh pial >> surface of >> >> a subject. When I use the freeview gui and select >> >> lh.aparc.a2009s.annot under the annotations menu a strange >> >> multicolored surface is loaded. It looks like something >> that has >> >> been tie-dyed and not like the examples of parcellation >> that are >> >> shown on some of the freesurfer pages. >> >> >> >> I have attached a screenshot of the output that I get. >> >> >> >> Any help would be appreciated. >> >> >> >> Thank you, >> >> >> >> Laura >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> The information in this e-mail is intended only for the >> person to whom it is >> >> addressed. If you believe this e-mail was sent to you in >> error and the e-mail >> >> contains patient information, please contact the Partners >> Compliance HelpLine at >> >> http://www.partners.org/complianceline . If the e-mail was >> sent to you in error >> >> but does not contain patient information, please contact >> the sender and properly >> >> dispose of the e-mail. >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >
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